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POM UNC > Amino Acid Metabolism > Flashcards

Amino Acid Metabolism Flashcards

1
Q

How are peptides held together?

A

Peptide bonds (carboxyl group of one amino acids binds with the amino group of another. Water is lost)

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2
Q

What is the general structure of an amino acid?

A

alpha carbon (carbon in the middle) is bound to a hydrogen, a side chain, an amino group (NH3+) and a carboxyl group (COO-)

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3
Q

What are the hydrophobic amino acids?

A

FAMILY VWPG - phenylalanine, alanine, methionine, isoleucine, leucine, tyrosine, valine, tryptophan, proline, glycine

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4
Q

What are the hydrophilic amino acids?

A

Histidine, Lysine, Asparagine, Arginine, Aspartic Acid, Serine, Cysteine, Threonine, Glutamic Acid, Glutamine,

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5
Q

What are the positive amino acids?

A

Arginine, Lysine, Histidine

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6
Q

What are the negative amino acids?

A

Aspartic Acid, Glutamic Acid

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7
Q

What are the branched amino acids?

A

Valine, isoleucine, leucine

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8
Q

What are essential vs. nonessential amino acids?

A

Essential amino acids are amino acids we need to eat. Nonessential amino acids are amino acids we can make, although we usually require essential amino acids to make the nonessential ones.

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9
Q

What are the essential amino acids?

A

Valine, Tryptophan, Isoleucine, Leucine, Lysine, Histidine, Methionine, Phenylalanine, Threonine (there are 9)

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10
Q

What are the nonessential amino acids?

A

11 nonessential: alanine, arginine, asparagine, aspartate, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine

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11
Q

What is the urea cycle?

A

Elimination of excess ammonium from the body in the form of urea. Urea cycle begins with the formation of carbonyl phosphate. Carbonyl phosphate is formed from CO2 and NH4+. NH4+ is usually captured by glutamate and released for the urea cycle by glutamate dehydrogenase. Carbonyl phosphate synthesis is catalyzed by carbonyl phosphate synthetase I. It takes 2 ATP. (CPSI will be the major enzyme for urea cycle regulation).
Next, carbonyl phosphate reacts with ornithine to form citrulline (by ornithine transcarbamoylase). Citrulline is able to pass through the mitochondrial membrane into the cytosol. Citrulline is converted to arginosuccinate (add aspartate + ATP, use arginosuccinate synthetase). Arginosuccinate is converted to fumarate (by arginosuccinate lyase) and arginine. Arginase is the enzyme that makes arginine
release a molecule of urea and become ornithine. ornithine is transported back into the mitochondria and reused.

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12
Q

How are most proteins degraded?

A

Urea cycle for the nitrogen group. Glycolysis or gluconeogenesis get rid of the carbon backbone.

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13
Q

Draw amino acid degradation

A

NH4+ –> (carbamoyl phosphate synthetase 1) –> carbamoyl phosphate
carbamoyl phosphate + ornithine -(ornithine trasncarbamoylase)-> citrulline
citrulline leaves mitochondria for cellular environment.
citrulline + aspartate + ATP –> (arginosuccinate synthetase) arginosuccinate + AMP
arginosuccinate –> (arginosuccinate lyase) fumarate.
fumarate –> arginine
arginine –>(arginase) ornithine + urea

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14
Q

What happens when you have an arginosuccinase deficiency?

A

Normally arginine –> ornithine is where urea is made. If you can’t go from arginosuccinate –> fumarate you can’t take ammonium from the body because ornithine isn’t regenerated. So if you cut past the deficiency and add arginine you’ll be able to provide ornithine, and ultimately the body excretes ammonium through arginosuccinate.

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15
Q

What are symptoms of having too much ammonia in your system?

A

Hyperammonemia - harmful to nervous system, can cause mental health disorders.

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16
Q

What happens when you have an ornithine transcarbamoylase or carbamoyl phosphate synthetase deficiency?

A

If you can’t form citrulline you can’t get rid of ammonia through the urea cycle. BUT! glycine and glutamine build up and you can treat that. Benzoate and phenylacetate will react with glycine and glutamine (respectively) and these molecules can be excreted.

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17
Q

Where can amino acids come from?

A

Our old proteins are recycled (turnover), and we consume proteins in our diets.

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18
Q

What are the steps of protein digestion in the gut?

A

HCL and pepsin in the stomach break down the protein into smaller peptide chains. Trypsinogen, chymotryspinogen and other zymogens from the pancreas act in the small intestine to break peptides into 2-3 amino acids chains. Aminopeptidases in the small intestine (di-tri peptidases) epithelial cells break these chains into individual amino acids, which are transported to the blood.

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19
Q

Which nonessential amino acids require essential amino acids for synthesis?

A

cysteine requires methionine, and tyrosine requires phenylalanine

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20
Q

What is a common reaction in the formation of amino acids?

A

Many amino acids are made by transamination between another amino acid and an alpha keto acid (amino acid donates amino group to new keto acid to form new amino acid)

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21
Q

What amino acids are produced from glutamate?

A

Glutamine, proline, arginine

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22
Q

What amino acids come from oxaloacetate?

A

aspartate and asparagine (although asparagine requires glutamine)

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23
Q

What amino acids come from serine?

A

glycine (side group is cleaved) and cysteine (although methionine is required)

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24
Q

What is a keto acid?

A

A keto acid is carbohydrate chain with a carboxylic acid and a ketone. an alpha keto acid means the ketone and carboxylic acid are adjacent to one another.

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25
Q

What is the transamination reaction?

A

Transfer amino group from alpha amino acid to an alpha keto acid. Catalyzed by aminotransferases, using pyridoxal phosphate as a cofactor (PLP). aminotransferase is named after the initial amino acid donating its amino group.

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26
Q

What is an example of a transamination reaction?

A

Aspartate + alpha ketoglutarate –> oxaloacetate + glutamate (aspartate has donated its amino group to alpha ketoglutarate, forming glutamate)

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27
Q

What is vitamin B6 used for in amino acid synthesis?

A

Pyridoxal phosphate (PLP) is derived from vitamin B6. PLP is actually the cofactor that transfers the amino group from the old amino acid to the keto acid. It’s used in all amination reactions AND is used in both the reactions to get from serine + homocysteine to cysteine.

28
Q

What glycolysis intermediate can be used to make glycine, serine, cysteine and alanine?

A

3-phosphoglycerate! It can be transformed into serine. Serine can turn into glycine or can create cysteine. Cysteine (or 2 phosphoglycerate if you continue glycolysis) can turn into pyruvate, and pyruvate can turn into alanine.

29
Q

How is serine turned into glycine?

A

Serine’s side group is cleaved by FH4 (tetrahydrofolate, also designated THF).

30
Q

What is tetrahydrofolate?

A

A one-carbon carrier used in a lot of amino acid synthesis reactions (Serine to glycine). Derived from vitamin B9 through a series of reactions that require NADPH (produced in pentose phosphate pathway and transfer of oxaloacetate back into the mitochondria). Tetrahydrofolate exists in many modified forms, which can all be converted between each other. Each carries alternate single-carbon units

31
Q

What is S-Adenosylmethionine?

A

SAM is derived from methionine. It’s a methyl donor group for many of the methyl containing compounds in the body. SAM is used for methylation of DNA and RNA and tRNA.

32
Q

How is methionine synthesized from S-adenosylmethionine?

A

SAM donates a methyl group to become S-adenosyl homocysteine. S-adenosyl homocysteine is converted into homocysteine. Homocysteine, through interactions with tetrahydrofolate (vitamin B9 derivative) and vitamin B12, becomes methionine. The reaction is catalyzed by methionine synthase.

Homocysteine can also be used to form cysteine through another pathway.

33
Q

How is cysteine formed?

A

Once homocysteine is formed out of methionine via SAM, it can be used with serine to form cysteine. Serine is made elsewhere. Homocysteine and Serine bind (with the loss of water) through cystathionine synthase (coactivated by pyridoxal phosphate, which is vitamin B6). Cystathionine gains a water, loses an ammonium, and loses an alpha-keto-butyrate (catalyzed by cystathionase and activated by PLP) to become cysteine.

34
Q

What is homocystinuria?

A

A defect in cystathionine synthase, which catalyzes the reaction from serine + homocysteine –> cystathionine. You end up with high concentrations of serine and homocysteine, and low concentrations of cysteine. At risk for intellectual disability and blood clots.

35
Q

How is cysteine production regulated?

A

Cysteine acts as a negative inhibitor of the reaction. More cysteine (product) will inhibit the action of cystathionine synthase

36
Q

What is hyperhomocysteinemia?

A

A condition with elevated homocysteine levels. Leads to cardiovascular and neurological diseases. Hyperhomocysteinemia can be caused by deficiencies in vitamin B12 (takes homocysteine to methionine with help of FH4) or FH4. Tetrahydrofolate is key in turning homocysteine into methionine (eliminating homocysteine). This is why pregnant women take folate supplements (to stop it from being an issue). Hyperhomocysteinemia can also be caused by a mutation in cystathionine synthase.

37
Q

How can homocysteine be cleared from the body?

A

Homocysteine has three pathways for removal. It can be converted into cystathionine and ultimately to cysteine. Or it can be turned into methionine through one of two pathways. First, homocysteine conversion to methionine is catalyzed by FH4 and vitamin b12. This is the major pathway. Alternatively, homocysteine can react with betaine to form methionine. But the betaine pathway is slow, and the cysteine reaction is regulated by the amount of cysteine present. So deficiencies in FH4 or vitamin B12 lead to excess cysteine and ultimately excess homocysteine (after the cysteine pathway shuts down)

38
Q

Draw the general diagram of which amino acids can be produced from TCA intermediates.

A

oxaloacetate –> aspartate. aspartate + glutamine –> asparagine

alphaketoglutarate –> glutamate
glutamate –> glutamine or proline or arginine

39
Q

How is glutamate made in the body?

A

Alphaketoglutarate undergoes a transamination reaction, which requires NADPH. NH4+ is donated to the alpha-ketoglutarate and a water is lost. Facilitated by glutamate dehydrogenase (because we’re making glutamate by dehydrating alphaketoglutarate)

40
Q

What amino acids are made from glutamate?

A

glutamine, proline (proline is made in a two step reaction from glutamate semialdehyde), arginine (arginine is made in the urea cycle)

41
Q

How is glutamine made?

A

It’s made from glutamate, facilitated by glutamine synthase (backwards by glutaminase). It takes ATP to make glutamine. A water is lost and an ammonium group is added.

42
Q

How is proline made?

A

Proline is made from glutamate. The reaction requires NADPH and ATP. Glutamate loses a hydroxyl ion to form glutamate semialdehyde (takes ATP). Glutamate semialdehyde spontaneously reorganizes into a cyclic molecule (pyrroline 5 carboxylate). NADPH is used to turn pyrroline 5 carboxylate to proline (reduce a double bond)

43
Q

How is aspartate formed?

A

Aspartate is formed from a transamination reaction between oxaloacetate and glutamate. Glutamate donates an ammonia group to oxaloacetate, forming aspartate. This reaction is catalyzed by aspartate aminotransferase, and facilitated by pyridoxal 5-phosphate

44
Q

How is asparagine formed?

A

Asparagine is formed from aspartate and glutamine. Aspartate loses a water group, steals an ammonia group from glutamine and becomes asparagine. Glutamine is turned back into glutamate. The reaction takes ATP and is facilitated by asparagine synthetase.

45
Q

How is tyrosine formed?

A

Tyrosine is derived from phenylalanine (both big rings and phenylalanine is an essential amino acids). The reaction requires oxygen and outputs water. Phenylalanine reacts with Tetrahydrobiopterin (BH4) to form BH2 and tyrosine. The reaction is facilitated by phenylalanine hydroxylase. replenishing BH4 takes NADH.

46
Q

What are the essential amino acids?

A

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine

47
Q

What are the nonessential amino acids?

A

alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine

48
Q

What is tyrosinemia 1?

A

A defect in furarylacetoacetate, the enzyme used to degrade tyrosine products into fumarate and acetoacetate.

49
Q

What is tyrosinemia 2?

A

A defect in tyrosine aminotransferase, which stops tyrosine from beginning its degradation process.

50
Q

What is alkaptonuria?

A

A defect in homogentisate oxidase, leads to a build up in homogentisate. Can cause joint pain.

51
Q

What are the steps of phenylalanine degradation?

A

Phenylalanine is turned into tyrosine by phenylalanine hydoxylase. Tyrosine is turned into p-Hydroxyphenylpyruvate by tyrosine aminotransferase. p-Hydroxyphenylpyruvate is turned into homogentisate. homogentisate is turned into fumarate and acetoacetate by combined action of homogentisate oxidase and fumarylacetoacetate hydrolase

52
Q

What is phenylketonuria?

A

You’re not able to produce tyrosine because of a defect in phenylalanine hydroxylase. Tyrosine is a critical intermediate for things like dopamine and other neurotransmitters. Without tyrosine you often have intellectual impairment. Phenylalanine builds up to toxic levels (20X normal). Solved by a low phenylalanine diet with a lot of tyrosine supplements.

53
Q

How are most amino acid synthesis reactions regulated?

A

The first step in the reaction is negatively regulated by the presence of the amino acid. Reaction progress/speed is regulated by availability/concentration of enzymes and substrates as well.

54
Q

How are the branched amino acids degraded?

A

Branched amino acids are first degraded into alpha keto acids by transamination. next they’re oxidatively decarboxylated (lose CO2 group) to propionyl CoA (valine and isoleucine) acetyl coa (isoleucine, leucine), and acetate (leucine). Oxidation is done by branched-chain dehydrogenase.

55
Q

What is maple syrup urine disorder?

A

Valine, Isoleucine, and Leucine are able to transition into alpha keto acids, but branched chain dehydrogenase (the enzyme used to oxidate the keto acids) is missing, so the alpha keto acids accumulate. If you don’t decrease your branched-chain intake you’ll end up with severe mental and physical disabilities.

56
Q

What are arginine, aspartate, glutamate, glutamine, glycine, histidine, serine, tryptophan, and tyrosine precursor molecules for?

A

Arginine: Nitric Oxide (used in vasodilation)
Aspartate: nucleotides
Glutamate: nucleotides, GABA (nervous system depression)
Glutamine: nucleotides
Glycine: heme groups (oxygen transports)
Histidine: Histamine (allergies)
Serine: sphingosine (lipid)
Tryptophan: NAD+, serotonin (neurotransmitter)
Tyrosine: L-DOPA, epinephrine, dopamine, melanin, thyroxine (regulation of metabolism in thyroid)

57
Q

Where do carbon atoms from degraded amino acids go?

A

Amino acids that break down into acetyl CoA or acetoacetyl CoA have their carbons used in the creation of ketone bodies.
Amino acids that break down into one of the intermediates in the TCA cycle or pyruvate have their carbons used to form glucose (assuming in both cases that the amino acids are not being recycled for new proteins.

58
Q

What is glutathione?

A

A tripeptide used to protect the body from oxidative damage.

59
Q

What is nitric oxide?

A

A signaling molecule derived from arginine. Its production requires 2 molecules of NADPH.

60
Q

Where do many of the carbons in heme groups (in RBCs) come from?

A

Breakdown of glycine.

61
Q

What is albinism?

A

You don’t have melanin. Most severe case is caused by defect in tyrosinase. Tyrosinase is an enzyme used to convert tyrosine into dopaquinone, which is a key molecule in the process of melanin synthesis.

62
Q

Draw the urea cycle

A

co2 + nh4+ + 2ATP –> (carbamoyl phosphate synthase I CPSI) –> carbamoyl phosphate + 2ADP
carbamoyl phosphate + ornithine –> (ornithine transcarbomylase) –> citrulline
citrulline + aspartate –> (arginosuccinate synthase) –> arginosuccinate
arginosuccinate –> (arginosuccinase) –> arginine + fumarase
arginine –> (arginase) –> ornithine + urea
ornithine is regenerated and reused in cycle

63
Q

Why do we have the urea cycle?

A

ammonia is a toxic byproduct of amino acid degradation. It needs to be eliminated from the body. The urea cycle turns ammonia into urea, which is non-toxic and can be peed out.

64
Q

Where does the urea cycle occur?

A

In the liver’s cells. Some of the reaction (carbamoyl phosphate synthesis and reaction with ornithine to make citrulline) occurs in the mitochondrial matrix. The rest occurs in the cytoplasm of liver cells.

65
Q

What is CPSI?

A

Carbamoyl Phosphate Synthase I (catalyzes reaction from Co2 + Nh4+ –> carbamoyl phosphate. irreversible step in urea production)

66
Q

What molecule in the urea cycle is reused?

A

Ornithine!

67
Q

How is CPSI regulated?

A

CPSI is regulated by N-acetylglutamate. You need N-acetylglutamate (NAG) present for CPSI to convert CO2 & nh4 –> carbamoyl phosphate. NAG is made by n-acetylglutamate synthase. NAG synthase is activated when glutamate and arginine (indicative of high NH4+ levels) are present. NAG

POM UNC (21 decks)

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